Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Has reproduction · 48
Prediction of Alzheimer's disease-specific phospholipase c gamma-1 SNV by deep learning-based approach for high-throughput screening.
PMID 33397809 · PMC7826347 · Proceedings of the National Academy of Sciences of the United States of America · 2021 · 7 claims · 7 setups
An AD-specific frameshift insertion SNV in exon 27 of mouse PLCγ1 causes abnormal exon skipping (exons 26-30) during mRNA maturation in 5xFAD cortex
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Has reproduction · 63
Community assessment of methods to deconvolve cellular composition from bulk gene expression.
PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups
Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.
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Has reproduction · 95
MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.
PMID 29901703 · PMC6025204 · GigaScience · 2018 · 6 claims · 7 setups
A two-step 'omni' RNA-seq pipeline (MetaMap) combining STAR human alignment with CLARK-S metagenomic classification can quantify archaeal, bacterial, and viral reads from the non-human read fraction of human RNA-seq data
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Has reproduction · 75
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.
PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups
AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 100
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.
PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 7 setups
A network-based meta-analysis of 27 discovery cohorts identified a common 45-gene signature specific to active TB disease across studies.
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Has reproduction
Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.
PMID 35672799 · PMC9175345 · Genome biology · 2022 · 8 claims · 7 setups
CD4+ T cells and B cells independently and significantly contribute to MS GWAS heritability enrichment, distinct from a merely shared immune regulatory landscape.
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Has reproduction · 45
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.
PMID 29451882 · PMC5815590 · PloS one · 2018 · 7 claims · 7 setups
This is the first de novo transcriptomic analysis of Cornus officinalis, providing fundamental gene and biosynthetic pathway information.
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Has reproduction · 90
Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart.
PMID 37012284 · PMC10070245 · Scientific reports · 2023 · 7 claims · 8 setups
Batch correction using sequencing platform as the correcting variable (via Combat-Seq) removes technical variability so that samples cluster by injury condition rather than dataset origin.
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Has reproduction · 50
Wx: a neural network-based feature selection algorithm for transcriptomic data.
PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups
The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.
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Has reproduction · 100
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.
PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups
WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features
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Has reproduction · 50
Dissecting lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.
PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 7 claims · 7 setups
LncRNA-mRNA competitive regulatory network topology and function differ substantially between control and cytokine-treated (IL-1β+IFN-γ) islet exosomes
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Has reproduction · 84
TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.
PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups
TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles
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Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO
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Has reproduction · 73
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.
PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups
Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.
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Has reproduction · 62
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.
PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups
Immature (day 7) CASK KO induced neurons show increased dendritic complexity/neurite overgrowth and upregulated gene networks for cell adhesion, neurite outgrowth, and cytoskeletal organization.
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Has reproduction · 67
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.
PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups
PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons
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Has reproduction · 85
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.
PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups
Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution
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Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 8 claims · 8 setups
CAI is positively correlated with translational efficiency, validating its use as a proxy for translational efficiency at the elongation level.
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Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups
AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)